# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1372079525 18000
# Node ID 1bc79c9d6165ae82c62d5c9a4c1ab1b1169561c0
# Parent  b649c729be4c7a32f2fba756f7db747e845fc253
Move tool-data/defuse.loc.sample to tool-data/defuse_reference.loc.sample

diff -r b649c729be4c -r 1bc79c9d6165 tool-data/defuse.loc.sample
--- a/tool-data/defuse.loc.sample	Mon Jun 24 07:01:48 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-## Configurstion info for prepared data references for DeFuse
-## http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
-## 3 columns separated by the TAB character
-## The 3rd column has dictionary values that will be substituted in the config file for defuse
-## It should likely contain keys:   dataset_directory gene_models genome_fasta repeats_filename est_fasta est_alignments unigene_fasta
-## If this is not a Homo_sapiens reference also need keys:  gene_id_pattern transcript_id_pattern chromosomes
-
-#db_key	name	{'config_key':'config_value'}
-#hg19	GRCh37(hg19)	{'gene_id_pattern':'ENSG\d+', 'transcript_id_pattern':'ENST\d+', 'dataset_directory':'/data/genomes/Hsapiens/hg19/defuse', 'gene_models':'$(dataset_directory)/Homo_sapiens.GRCh37.62.gtf', 'genome_fasta':'$(dataset_directory)/Homo_sapiens.GRCh37.62.dna.chromosome.fa', 'repeats_filename':'$(dataset_directory)/rmsk.txt', 'est_fasta':'$(dataset_directory)/est.fa', 'est_alignments':'$(dataset_directory)/intronEst.txt', 'unigene_fasta':'$(dataset_directory)/Hs.seq.uniq', 'chromosomes':'1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT', 'mt_chromosome':'MT', 'gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding', 'ig_gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene', 'rrna_gene_sources':'Mt_rRNA,rRNA,rRNA_pseudogene'}
-#mm9	NCBIM37(mm9)	{'gene_id_pattern':'ENSMUSG\d+', 'transcript_id_pattern':'ENSMUST\d+', 'dataset_directory':'/data/genomes/Mmusculus/mm9/defuse', 'gene_models':'$(dataset_directory)/Mus_musculus.NCBIM37.63.gtf', 'genome_fasta':'$(dataset_directory)/Mus_musculus.NCBIM37.63.dna.chromosome.fa', 'repeats_filename':'$(dataset_directory)/rmsk.txt', 'est_fasta':'$(dataset_directory)/est.fa', 'est_alignments':'$(dataset_directory)/intronEst.txt', 'unigene_fasta':'$(dataset_directory)/Mm.seq.uniq', 'chromosomes':'1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT', 'mt_chromosome':'MT', 'gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding', 'ig_gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene', 'rrna_gene_sources':'Mt_rRNA,rRNA,rRNA_pseudogene'}
-#mm8	NCBIM36(mm8)	{'gene_id_pattern':'ENSMUSG\d+', 'transcript_id_pattern':'ENSMUST\d+', 'dataset_directory':'/data/genomes/Mmusculus/mm9/defuse', 'gene_models':'$(dataset_directory)/Mus_musculus.NCBIM36.46.gtf', 'genome_fasta':'$(dataset_directory)/Mus_musculus.NCBIM36.46.dna.chromosome.fa', 'repeats_filename':'$(dataset_directory)/rmsk.txt', 'est_fasta':'$(dataset_directory)/est.fa', 'est_alignments':'$(dataset_directory)/intronEst.txt', 'unigene_fasta':'$(dataset_directory)/Mm.seq.uniq', 'mt_chromosome':'MT', 'gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding', 'ig_gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene', 'rrna_gene_sources':'Mt_rRNA,rRNA,rRNA_pseudogene'}
diff -r b649c729be4c -r 1bc79c9d6165 tool-data/defuse_reference.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/defuse_reference.loc.sample	Mon Jun 24 08:12:05 2013 -0500
@@ -0,0 +1,7 @@
+## Configurstion info for prepared data references for DeFuse
+## http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.0
+## 4 columns separated by the TAB character
+## The 4th column has the path to the defuse config.txt file, it needs to have the dataset_directory set the directory path where the defuse reference data resides.
+## The defuse galaxy tool  will substitute the directory path of config.txt if the dataset_directory property is not set '__DATASET_DIRECTORY__'
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
+GRCh37	GRCh37	Human GRCh37 (hg19)	/depot/GRCh37/defuse/GRCh37.config